I can confirm this bug and unfortanetly, Daniels suggestion doesn't work
:(

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https://bugs.launchpad.net/bugs/893992

Title:
  Messaging Indicator does not go blue on new mail in Thunderbird IMAP
  account

Status in “thunderbird” package in Ubuntu:
  Confirmed

Bug description:
  My Thunderbird is configured to connect via LAN to my college IMAP server. 
When a new mail arrives, there is only a system notification saying a new mail 
has arrived. The Messaging Indicator envelope does not turn blue. Neither does 
the Thunderbird icon in the Unity Launcher show unread mail count. So if I miss 
the notification because I was looking away, I do not have a way of knowing 
that a mail has arrived.
  I have tried purging the whole package including the ~/.thunderbird folder, 
but the problem refuses to go. Messaging menu works fine because Empathy and 
gm-notify both use it without any trouble.

  ProblemType: Bug
  DistroRelease: Ubuntu 11.10
  Package: thunderbird 7.0.1+build1+nobinonly-0ubuntu1
  ProcVersionSignature: Ubuntu 3.0.0-13.22-generic 3.0.6
  Uname: Linux 3.0.0-13-generic x86_64
  NonfreeKernelModules: fglrx
  AddonCompatCheckDisabled: False
  AlsaVersion: Advanced Linux Sound Architecture Driver Version 1.0.24.
  ApportVersion: 1.23-0ubuntu4
  Architecture: amd64
  ArecordDevices:
   **** List of CAPTURE Hardware Devices ****
   card 0: Intel [HDA Intel], device 0: STAC92xx Analog [STAC92xx Analog]
     Subdevices: 1/1
     Subdevice #0: subdevice #0
  AudioDevicesInUse:
   USER        PID ACCESS COMMAND
   /dev/snd/controlC1:  nishant    3909 F.... pulseaudio
   /dev/snd/controlC0:  nishant    3909 F.... pulseaudio
   /dev/snd/pcmC0D0p:   nishant    3909 F...m pulseaudio
  BuildID: 20110929183320
  CRDA: Error: [Errno 2] No such file or directory
  Card0.Amixer.info:
   Card hw:0 'Intel'/'HDA Intel at 0xfc500000 irq 46'
     Mixer name : 'IDT 92HD73C1X5'
     Components : 'HDA:111d7675,102802be,00100103'
     Controls      : 16
     Simple ctrls  : 10
  Card1.Amixer.info:
   Card hw:1 'HDMI'/'HDA ATI HDMI at 0xfc010000 irq 48'
     Mixer name : 'ATI R6xx HDMI'
     Components : 'HDA:1002aa01,00aa0100,00100100'
     Controls      : 4
     Simple ctrls  : 1
  Card1.Amixer.values:
   Simple mixer control 'IEC958',0
     Capabilities: pswitch pswitch-joined penum
     Playback channels: Mono
     Mono: Playback [on]
  Channel: release
  Date: Wed Nov 23 18:49:25 2011
  ForcedLayersAccel: False
  IfupdownConfig:
   auto lo
   iface lo inet loopback
  InstallationMedia: Ubuntu 11.10 "Oneiric Ocelot" - Beta amd64 (20110921.2)
  IpRoute:
   default via 172.24.71.254 dev eth0  proto static 
   169.254.0.0/16 dev eth0  scope link  metric 1000 
   172.16.138.0/24 dev vmnet1  proto kernel  scope link  src 172.16.138.1 
   172.24.64.0/21 dev eth0  proto kernel  scope link  src 172.24.64.19  metric 
1 
   192.168.150.0/24 dev vmnet8  proto kernel  scope link  src 192.168.150.1
  Prefs:
   extensions.lastAppVersion - 7.0.1
   network.cookie.prefsMigrated - true
   font.size.variable.x-western - 12
   plugin.soname.list - libXext.so
  Profiles: Profile0 (Default) - LastVersion=7.0.1/20110929183320 (Running)
  RunningIncompatibleAddons: False
  SourcePackage: thunderbird
  UpgradeStatus: No upgrade log present (probably fresh install)
  dmi.bios.date: 11/07/2009
  dmi.bios.vendor: Dell Inc.
  dmi.bios.version: A08
  dmi.board.vendor: Dell Inc.
  dmi.board.version: A08
  dmi.chassis.type: 8
  dmi.chassis.vendor: Dell Inc.
  dmi.chassis.version: A08
  dmi.modalias: 
dmi:bvnDellInc.:bvrA08:bd11/07/2009:svnDellInc.:pnStudio1555:pvrA08:rvnDellInc.:rn:rvrA08:cvnDellInc.:ct8:cvrA08:
  dmi.product.name: Studio 1555
  dmi.product.version: A08
  dmi.sys.vendor: Dell Inc.

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